Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution

Perkins, Stephen J.; Dwek, Raymond A.

doi:10.1021/bi00543a001

Cited by 93 publications

(55 citation statements)

References 43 publications

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“…Other estimates have come from empirical studies of shifts in organic and protein systems (Perkins and Dwek, 1980;Abraham, 1981;Cross and Wright, 1985;Osapay and Case, 1991). Many of the ringcurrent intensities determined here are larger than the earlier values, although the general trends in the values are often preserved; for example, both new and old calculations predict pyrimidine bases to have much smaller ring currents than purines, and phenylalanine to have larger currents than tyrosine.…”

Section: Results For Aromatic Ringsmentioning

confidence: 69%

Calibration of ring-current effects in proteins and nucleic acids

1995

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Density functional chemical shielding calculations are reported for methane molecules placed in a variety of positions near aromatic rings of the type found in proteins and nucleic acids. The results are compared to empirical formulas that relate these intermolecular shielding effects to magnetic anisotropy ('ring-current') effects and to electrostatic polarization of the C-H bonds. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of the ring-current intensity factors for aromatic amino acids and nucleic acid bases. Electrostatic interactions contribute significantly to the computed chemical shift dispersion. Prospects for using this information in the analysis of chemical shifts in proteins and nucleic acids are discussed.

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Section: Results For Aromatic Ringsmentioning

confidence: 69%

Calibration of ring-current effects in proteins and nucleic acids

1995

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“…The ring current shift calculations have been based on the intensity factors of Giessner-Prettre and Pullman [18]. A new set of ring current intensity factors for tryptophan has been proposed by Perkins and Dwek [29]. These intensity factors were obtained by regression analysis using data for 45 aliphatic and aromatic resonances of hen lysozyme [29].…”

Section: Discussionmentioning

confidence: 99%

“…A new set of ring current intensity factors for tryptophan has been proposed by Perkins and Dwek [29]. These intensity factors were obtained by regression analysis using data for 45 aliphatic and aromatic resonances of hen lysozyme [29]. A decrease in the RMS difference of about 15% was found when tryptophan intensity factors of 1.…”

Section: Discussionmentioning

confidence: 99%

Assignment of resonances in the ¹H NMR spectrum of human lysozyme

Boyd

Dobson

Redfield

1985

European Journal of Biochemistry

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Assignments in the IH NMR spectrum for more than 120 resonances arising from 38 of the 130 amino acid residues of human lysozyme are presented. Assignments have been achieved using a combination of one and twodimensional NMR techniques. Two-dimensional double-quantum correlated spectroscopy and relayed coherence transfer spectroscopy were found to be particularly useful for the identification of spin systems in the aromatic and methyl regions of the spectrum. These spin systems were assigned to specific residues in human lysozyme with reference to the X-ray crystal structure using one-dimensional nuclear Overhauser enhancement (NOE) data and a computer-based search procedure. Unique assignments were found for resonances of 27 amino acid residues even when a distance constraint on NOE effects of 0.7 nm was used in the search procedure; for the remaining residues closer constraints or additional information were required. The assignments include all but one of the resonances in the aromatic region of the spectrum and all the methyl group resonances in the region upfield of 0.6 ppm. The assignments presented here provide a basis for a comparison of the NMR spectra of human lysozyme and the more widely studied hen lysozyme.Human lysozyme is a protein composed of 130 amino acid residues found in a variety of secretions including milk, tears and saliva [I]. It differs from the more widely studied hen lysozyme in about 40% of its sequence. These differences include 51 amino acid substitutions and the insertion of a glycine residue at position 48. The X-ray structure of human lysozyme has been refined at a resolution of 0.15 nm [2, 31 and resembles that of hen lysozyme very closely despite the large number of amino acid substitutions. The RMS difference in C" positions is only 0.074 nm and the hydrogen bonding interactions in the two proteins are very similar [ 3 ] . Of the 51 amino acid differences between hen and human lysozymes, 41 correspond to amino acids on the surface of the protein. The catalytically important residues Glu-35 and Asp-53 are conserved but there are several substitutions in the active-site region which could affect substrate binding [I]. Many differences between the sequences of hen and human lysozymes involve aromatic amino acids. For example, human lysozyme contains six tyrosine residues whereas hen lysozyme contains only three.The NMR spectrum of hen lysozyme has been studied previously in considerable detail, and assignments of more than 160 resonances of 47 amino acid residues have been reported [4 -71. The large number of amino acid differences between hen and human lysozymes result in NMR spectra Correspondence to C . M. Dobson, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, England OX1 3QRAbbreviafions. COSY, two dimensional homonuclear correlated spectroscopy; RCT, relayed coherence transfer spectroscopy; NOE, nuclear Overhauser enhancement; LV, leucine or valine; AT, alanine or threonine; 1 D, one-dimensional ; 2 D, two-dimensional; RMS, root mean square;...

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“…The ring-current shift 6, caused by the aromatic residues was approximated using the dipolar equation [20] with the normalisation of Perkins et al [21]. For the six-membered and five-membered rings of adenine the ring-current intensity factors of 0.90 and 0.66, respectively, were used [22].…”

Section: Estimation Of the Range Of The Adenyl Ring-current Effertmentioning

confidence: 99%

The Structural Isomerisation of Human‐Muscle Adenylate Kinase as Studied by ¹H‐Nuclear Magnetic Resonance

Kalbitzer

Marquetant

Rösch

et al. 1982

European Journal of Biochemistry

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Human muscle adenylate kinase (ATP : AMP phosphotransferase, EC 2.7.4.3.) was studied by 'H-nuclear magnetic resonance spectroscopy. The C-2 and C-4 proton resonances of the active-center histidine His-36 could be identified; the p K o f His-36 was determined as 6.1. The pK of His-189 is very low (4.9) although it is located at the surface of the protein. Other resonance lines are discussed in comparison with N M R spectra of porcine adenylate kinase [McDonald et al. (1975) J . Biol. Chem. 250, 6947-69541. A pH-dependent structural isomerization as shown by X-ray crystallography in the pig enzyme [Pai et al. (1977) J . Mol. Biol. 114,[37][38][39][40][41][42][43][44][45] was not observed for human adenylate kinase in solution. However, the binding of adenosine(5')pentaphospho(5')adenosine (Ap,A), a bisubstrate inhibitor, to adenylate kinase causes an overall change of the N M R spectrum indicative of a large conformational change of the enzyme. The exchange rate (koff) for Ap,A was estimated as 10 s-' and decreases by addition of Mg2+. On the basis of these values and the known dissociation constant it is likely that the binding of Ap,A is a diffusion-controlled process, k,, being lo8 M -' s -. In conclusion, the system Ap,A/Mg2 +/human adenylate kinase, which has been studied by NMR spectroscopy and Xray diffraction in parallel, is suitable for analysing the induced fit postulated by Jencks for all kinase-catalyzed reactions.Jencks [I] has postulated that all ATP-dependent phosphotransferases must undergo a substrate-induced structural isomerization, that is an induced fit, in order to avoid the hydrolysis of ATP as a side-reaction. For a detailed study of this hypothesis, mammalian muscle adenylate kinase [2, 31 which catalyses the reaction MgATP+AMP + MgADP +ADP (EC 2.7.4.3) is a suitable protein because it is small ( M , = 22000) and monomeric and because its structure is known in atomic detail [4, 51. Moreover, as revealed by X-ray crystallography, reversible structural isomerizations do occur in this enzyme: depending on the pH of the mother liquor, crystalline porcine adenylate kinase exists in form C below pH 5.4, in conformation B between pH 5.7 and 6.0, and in conformation A between pH 6.9 and 8.0. The epicenter of the conformational change of B + A is Ser-19 which moves by 0.6 nm [6]. Pai et al. [7] have suggested that conformation B is related to the free enzyme E whereas conformation A is related to E*, the enzyme species after a substrate-induced conformational change. Crystalline human adenylate kinase is isomorphous with conformation B of porcine adenylate kinase in the pH range 5.5-7.7, a transition to form A and or above neutral pH could not be observed [8]. The present report deals with the conformation(s) of human adenylate kinase in solution using 'H-NMR spectroscopy. The reasons for choosing the human enzyme, which differs in 9 out of 194 residues from the porcine enzyme [S], were as follows. (a) Since X-ray diffraction analysis had failed to reveal different conformations of the human en...

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Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution

Cited by 93 publications

References 43 publications

Calibration of ring-current effects in proteins and nucleic acids

Calibration of ring-current effects in proteins and nucleic acids

Assignment of resonances in the ¹H NMR spectrum of human lysozyme

The Structural Isomerisation of Human‐Muscle Adenylate Kinase as Studied by ¹H‐Nuclear Magnetic Resonance

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Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution

Cited by 93 publications

References 43 publications

Calibration of ring-current effects in proteins and nucleic acids

Calibration of ring-current effects in proteins and nucleic acids

Assignment of resonances in the 1H NMR spectrum of human lysozyme

The Structural Isomerisation of Human‐Muscle Adenylate Kinase as Studied by 1H‐Nuclear Magnetic Resonance

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Assignment of resonances in the ¹H NMR spectrum of human lysozyme

The Structural Isomerisation of Human‐Muscle Adenylate Kinase as Studied by ¹H‐Nuclear Magnetic Resonance